The expansion of irrigated agriculture and the overexploitation of groundwater aquifers are leading to seawater intrusion and severe deterioration of groundwater quality at coastal areas. The shortage of good quality water resources constitutes an important threat for the maintenance of productivity of crops and soil protection. In the region of Marathon in Attica, an area with fast urbanization and intense agricultural activity, a network of 56 observation boreholes for monitoring water level and the qualitative characteristics of groundwater was installed. The values of EC, pH, Eh, as well as main anions and cations were determined twice, at the end of rainy and dry periods. Severe deterioration of water quality, due to high salt loads, was recorded, especially in areas very close to the sea. The possible risk for the crops and the soil, deriving from irrigation use of groundwater, was estimated. In certain regions, increased nitrate concentrations were observed due to intense use of fertilizers. The recent prevailing groundwater quality status was compared to that of the previous decade, revealing no significant further degradation of the coastal aquifer, except for some sub-areas.